The Drakes Bay Oyster Co. filed a motion in the Marin Superior Court Monday requesting a reconsideration of a judge's ruling made against the operation earlier this month.

In February the California Coastal Commission unanimously approved cease-and-desist and restoration orders against the oyster company, operated by Kevin Lunny, citing several violations of the state's Coastal Act.

Earlier this month Judge Lynn Duryee ruled that elements of the commission's order will have to be imposed. That will require Drakes Bay to address invasive Manila clams on its property, manage its invasive sea squirts — dubbed "marine vomit" — and the company's plastic debris.

Other aspects of the commission's order are under consideration by Duryee and will not be formally addressed pending the outcome of federal litigation on larger issues surrounding a federal decision not to offer a lease to Drakes Bay.

But Drakes Bay is fighting back, saying the commission's allegations are wrong and that Duryee should reconsider her ruling.

"These misrepresentations by the Coastal Commission are the same false charges that have been leveled for years by the Park Service," Lunny said in a written statement. "Those allegations have been repeatedly proven false by the nation's top scientists, and many are refuted by the Commission's own reports. We respectfully request that the court consider all of the evidence before making its final decision."

Among Drakes Bay's assertions:

 It has not exceeded the shellfish-production limits of a consent order issued in 2007.

 Its boats don't get too close to harbor seals.

 It is not "throwing its garbage" into Drakes Estero as the commission alleges, rather plastic materials that wash up on shore come from the previous owner and the ocean. Drakes Bay has a program in place for collecting and disposing of the debris as part of its stewardship program.

 The ecology of Drakes Estero is not being harmed by oyster operations.

Coastal Commission officials could not be reached for comment, but have stood by their allegations.

"This is nothing new, it's another attempt for Drakes Bay to paint themselves as victims," said Amy Trainer, executive director of the Environmental Action Committee of West Marin. "There is plenty of hard evidence to show the ecology of the estero has been damaged from their commercial operation."